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comparison build/tools/ExtractAnnotations/ExtractAnnotations.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
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10:6a112eaf8f38 11:40c15b7467f1
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="2.0.0"> 2 <tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="2.0.1">
3 <description>Extract databases' references from SBML annotations or notes.</description> 3 <description>Extract databases' references from SBML annotations or notes.</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractAnnotations -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractAnnotations -i "$inputPath"
11 -export "$export" 11 -export "$export"
12 -db "$db" 12 -db "$db"
13 $uniq 13 $uniq
32 <outputs> 32 <outputs>
33 <data format="tsv" name="outputPath"/> 33 <data format="tsv" name="outputPath"/>
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <test> 36 <test>
37
37 <param name="inputPath" value="Human-GEM_pathways.xml"/> 38 <param name="inputPath" value="Human-GEM_pathways.xml"/>
39
38 <param name="export" value="METABOLITE"/> 40 <param name="export" value="METABOLITE"/>
41
39 <param name="db" value="metanetx.chemical"/> 42 <param name="db" value="metanetx.chemical"/>
43
40 <output ftype="tsv" name="outputPath"> 44 <output ftype="tsv" name="outputPath">
45
41 <assert_contents> 46 <assert_contents>
47
42 <has_n_lines n="146"/> 48 <has_n_lines n="146"/>
49
43 <has_n_columns n="2"/> 50 <has_n_columns n="2"/>
51
44 </assert_contents> 52 </assert_contents>
53
45 </output> 54 </output>
55
46 </test> 56 </test>
47 <test> 57 <test>
58
48 <param name="inputPath" value="Human-GEM_pathways.xml"/> 59 <param name="inputPath" value="Human-GEM_pathways.xml"/>
60
49 <param name="export" value="METABOLITE"/> 61 <param name="export" value="METABOLITE"/>
62
50 <param name="db" value="metanetx.chemical"/> 63 <param name="db" value="metanetx.chemical"/>
64
51 <param name="skip" value="true"/> 65 <param name="skip" value="true"/>
66
52 <output ftype="tsv" name="outputPath"> 67 <output ftype="tsv" name="outputPath">
68
53 <assert_contents> 69 <assert_contents>
70
54 <has_n_lines n="145"/> 71 <has_n_lines n="145"/>
72
55 <has_n_columns n="2"/> 73 <has_n_columns n="2"/>
74
56 </assert_contents> 75 </assert_contents>
76
57 </output> 77 </output>
78
58 </test> 79 </test>
59 <test> 80 <test>
81
60 <param name="inputPath" value="Human-GEM_pathways.xml"/> 82 <param name="inputPath" value="Human-GEM_pathways.xml"/>
83
61 <param name="export" value="METABOLITE"/> 84 <param name="export" value="METABOLITE"/>
85
62 <param name="db" value="metanetx.chemical"/> 86 <param name="db" value="metanetx.chemical"/>
87
63 <param name="skip" value="true"/> 88 <param name="skip" value="true"/>
89
64 <param name="uniq" value="true"/> 90 <param name="uniq" value="true"/>
91
65 <output ftype="tsv" name="outputPath"> 92 <output ftype="tsv" name="outputPath">
93
66 <assert_contents> 94 <assert_contents>
95
67 <has_n_lines n="111"/> 96 <has_n_lines n="111"/>
97
68 <has_n_columns n="2"/> 98 <has_n_columns n="2"/>
99
69 </assert_contents> 100 </assert_contents>
101
70 </output> 102 </output>
103
71 </test> 104 </test>
72 </tests> 105 </tests>
73 <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri.]]></help> 106 <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri.]]></help>
74 <citations/> 107 <citations/>
75 </tool> 108 </tool>